Version 4.0 (R2011b) SimBiology Software

This table summarizes what's new in Version 4.0 (R2011b):

New Features and Changes	Version Compatibility Considerations	Fixed Bugs and Known Problems
Yes Details below	Yes—Details labeled as Compatibility Considerations, below. See also Summary.	Bug Reports Includes fixes

New features and changes introduced in this version are:

• Redesigned and Enhanced Desktop

• Open Projects in the Desktop from the Command Line

• New Covariate Class, Properties, and Methods

• Population Fitting Better Supports Covariate Analysis

• Fitting Functions Enhancements

• Parameter Estimation Enhancements

• Enhancements to Sensitivity Analysis

• Additional Syntax Checking of Reaction Rates, Rule Assignments, Event Triggers, and Event Functions

• Annotation Property Being Removed

• Function Elements Being Removed

Redesigned and Enhanced Desktop

The SimBiology desktop is redesigned to better support streamlined, iterative workflows. It no longer includes a Project Explorer to navigate between models, tasks, and data. Now, use the following management and navigation aids for projects and libraries:

• Toolstrip — Displays the HOME tab and other tabs depending on what you select in the address bar.

• HOME tab — Open and manage projects, including adding models, analysis tasks, and data to a project.

• Address bar — Select a project, model, task, or data to view and edit in the desktop window. Navigate between models, tasks, and data. Select and view libraries.

• Actions button — Use to select actions appropriate for the item (project, model, task, data, or library) selected and displayed in the desktop.

Tip   Selecting Project in the address bar displays all models, tasks, and data included in the project.

The MODEL, TASK, and DATA tabs better support the following iterative workflows:

• Model-centric workflow — Refine a model by performing iterative edits on the model. Without leaving the model, run multiple tasks and view results to help guide you with your model edits.

• Task-centric workflow — Refine an analysis task by performing iterative runs and edits on the task. Without leaving the task, select different models to run the task on. For example, select different models for a parameter fit task to find the model that best fits the data.

• Data-centric workflow — Plot and explore data, all from the DATA tabs.

For more information, see Getting Started Using the SimBiology Desktop.

Open Projects in the Desktop from the Command Line

The simbiology function is updated with a new syntax that lets you open projects (sbproj files) in the SimBiology desktop from the command line.

New Covariate Class, Properties, and Methods

There is a new CovariateModel class and related properties and methods that replace the existing PKCovariateModel class and related properties and methods, to perform covariate analysis for continuous covariates. The new CovariateModel class lets you specify initial estimates as parameters in the covariate expression, instead of embedding them in the covariate expression. For details, see Specifying a Covariate Model and the demo, Modeling the Population Pharmacokinetics of Phenobarbital in Neonates.

The construct method of the PKModelDesign class now returns a CovariateModel object with default expression information.

The PKData class includes a new method, getCovariateData, which returns only the covariate data from a data set.

Compatibility Considerations

The PKCovariateModel class and its related properties and methods now return warnings and will be removed in a future release. Use the CovariateModel class and related properties and methods instead.

Population Fitting Better Supports Covariate Analysis

The sbionlmefit and sbionlmefitsa functions accept the new CovariateModel object.

The sbionlmefit and sbionlmefitsa functions now return results that are better annotated. The results output structure now includes new fields with more descriptive names. For details on the new fields, see the sbionlmefit and sbionlmefitsa reference pages.

Compatibility Considerations

The following syntaxes that accept a PKCovariateModel object will be removed in a future release:

results = sbionlmefit(modelObj, pkModelMapObject, pkDataObject, pkCovModel)

results = sbionlmefitsa(modelObj, pkModelMapObject, pkDataObject, pkCovModel)

Instead, use these syntaxes that accept a CovariateModel object:

results = sbionlmefit(modelObj, pkModelMapObject, pkDataObject, CovModel)

results = sbionlmefitsa(modelObj, pkModelMapObject, pkDataObject, CovModel)

The following fields in the results output structure returned by sbionlmefit and sbionlmefitsa will be removed in a future release. Use the new fields instead:

Removed Field	New Field
estimate	FixedEffects
phiP	PopulationParameterEstimates
phiI	IndividualParameterEstimates
beta	FixedEffects
psi	RandomEffectCovarianceMatrix
b	RandomEffects

Support for the following name-value pair arguments used by sbionlmefit and sbionlmefitsa has changed:

• FEGroupDesign — You can no longer set this argument. It is computed from the covariate model.

• ParamTransform — If using the syntax that accepts a CovariateModel object, you can no longer set this argument. It is computed from the covariate model.

• REParamSelect — If using the syntax that accepts a CovariateModel object, you can no longer set this argument. It is computed from the covariate model.

Fitting Functions Enhancements

The following fitting functions now return standard errors. These functions also now run faster when estimating parameters of most common PK models:

• sbionlinfit — Perform nonlinear least-squares regression using SimBiology models

• sbionlmefit — Estimate nonlinear mixed effects using SimBiology models

• sbionlmefitsa — Estimate nonlinear mixed effects with stochastic EM algorithm

Compatibility Considerations

The first output argument of sbionlinfit is now an array of objects instead of an array of structures. The properties of the object are the same as the fields in the previous structure, with the following exceptions:

• The estimate field will be removed in a future release. Instead, use the ParameterEstimates property, which includes fitted coefficients and their standard errors.

• There is a new property, CovarianceMatrix, which contains the estimated covariance matrix for the fitted coefficients.

Parameter Estimation Enhancements

The sbioparamestim function is more robust and accurate due to the addition of the FinDiffRelStep field in the method input argument.

Compatibility Considerations

The method input for the sbioparamestim function has changed. Most important, when method uses the lscurvefit, lsqnonlin, or fmincon function, there is an additional field, FinDiffRelStep. For details on this new field, see the sbioparamestim reference page.

Also, when method uses the lscurvefit or lsqnonlin function, the DiffMinChange field now uses the same defaults as lscurvefit or lsqnonlin. Likewise, when method uses the fmincon function, the TypicalX field now uses the same default as fmincon.

Enhancements to Sensitivity Analysis

Models containing repeated assignment rules, rate rules, or doses now support sensitivity analysis. Also, you can now use parameters as outputs when performing sensitivity analysis.

Compatibility Considerations

The ParameterInputFactors and SpeciesInputFactors properties of the SensitivityAnalysisOptions property of the Configset object will be removed in a future release. Instead, use the new Inputs property.

Also, the SpeciesOutput property of the SensitivityAnalysisOptions property of the Configset object will be removed in a future release. Instead, use the new Outputs property.

Additional Syntax Checking of Reaction Rates, Rule Assignments, Event Triggers, and Event Functions

Model verification and simulation now perform additional syntax checks on reaction rates, rule assignments, event triggers, and event functions. These checks ensure all expressions simulate properly.

Compatibility Considerations

If an expression for a reaction rate, rule assignment, event trigger, or event function ends in any of the following, it now returns an error during verification or simulation:

• Semicolon

• Comma

• Comment text preceded by %

• Line continuations indicated by ...

Annotation Property Being Removed

Compatibility Considerations

The Annotation property of the following objects will be removed in a future version:

• AbstractKineticLaw

• Compartment

• ConfigSet

• Event

• KineticLaw

• Model

• Parameter

• Reaction

• RepeatDose

• Rule

• ScheduleDose

• Species

• Unit

Function Elements Being Removed

Function Elements Being Removed

Function Element Name	What Happens When You Use This Function Element	Use This Instead	Compatibility Considerations
PKCovariateModel object and related properties and methods	Warns	CovariateModel class and related properties and methods	See the Compatibility Considerations subheading in New Covariate Class, Properties, and Methods.
estimate and beta fields in the results structure returned by sbionlmefit or sbionlmefitsa	Warns	FixedEffects field	See the Compatibility Considerations subheading in Population Fitting Better Supports Covariate Analysis.
phiP field in the results structure returned by sbionlmefit or sbionlmefitsa	Warns	PopulationParameterEstimates field	See the Compatibility Considerations subheading in Population Fitting Better Supports Covariate Analysis.
phiI field in the results structure returned by sbionlmefit or sbionlmefitsa	Warns	IndividualParameterEstimates field	See the Compatibility Considerations subheading in Population Fitting Better Supports Covariate Analysis.
psi field in the results structure returned by sbionlmefit or sbionlmefitsa	Warns	RandomEffectCovarianceMatrix field	See the Compatibility Considerations subheading in Population Fitting Better Supports Covariate Analysis.
b field in the results structure returned by sbionlmefit or sbionlmefitsa	Warns	RandomEffects field	See the Compatibility Considerations subheading in Population Fitting Better Supports Covariate Analysis.
estimate field in the results structure returned by sbionlinfit	Warns	ParameterEstimates property of the results object returned by sbionlinfit	See the Compatibility Considerations subheading in Fitting Functions Enhancements.
Annotation property of SimBiology objects	Warns	—	See the Compatibility Considerations subheading in Annotation Property Being Removed.
ParameterInputFactors and SpeciesInputFactors properties of the SensitivityAnalysisOptions property of the Configset object	Warns	Inputs property of the SensitivityAnalysisOptions property of the Configset object	See the Compatibility Considerations subheading in Enhancements to Sensitivity Analysis.
SpeciesOutput property of the SensitivityAnalysisOptions property of the Configset object	Warns	Outputs property of the SensitivityAnalysisOptions property of the Configset object	See the Compatibility Considerations subheading in Enhancements to Sensitivity Analysis.

Version 4.1 (R2012a) SimBiology Software

Version 3.4 (R2011a) SimBiology Software

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